Southampton were ahead just before half-time when Kevin Phillips headed home from a centre by Graeme Le Saux after a hectic first period.
Boro could have been ahead by then, but Jimmy Floyd Hasselbaink shot at goalkeeper Antti Niemi, who also made a smart double save from Michael Reiziger and Mark Viduka.
At the other end Phillips shot wide from close range, half expecting to be given offside but Southampton were worthy of their interval lead.
Southampton looked as if they would be uncatchable when, after 64 minutes, Peter Crouch headed in a corner from the left by Le Saux.
Redknapp had handed Crouch his first Premiership starting chance and he responded with a superb display which should have earned him another goal four minutes later.
Le Saux, playing as a wing-back, floated into the centre from the left and Crouch somehow headed over with the goal at his mercy.
Anders Svensson ran unattended from midfield before shooting wide from the edge of the area but the longer the match went on, the stronger Middlesbrough became.
Viduka shot wide, as did George Boateng before Middlesbrough were handed an unexpected chance to snatch a point with an own goal a minute from time.
Stewart Downing took an inswinging corner from the right and Danny Higginbotham could only turn the ball over his own line to breathe new life into the match.
Injury-time had already been signalled when Middlesbrough went forward once more with fierce determination, sensing Southampton's unease and a minute into time added on the equaliser came.
Reiziger played the ball in from the right and Downing got it on to his left foot before smashing home a powerful low shot from 20 yards which gave Niemi no chance of saving.
Earlier Niemi had made an incredible save after Downing had ghosted in behind his markers, but from point-blank range his shot was somehow pushed away by the Finnish international goalkeeper to preserve Southampton's precarious lead.
But there was nothing Niemi could have done to keep out Downing's equaliser to leave Southampton shattered at the final whistle.
Redknapp, given a rousing reception by the crowd on his first appearance at St. Mary's, scuffed the ground in disgust at the final whistle having watched his side throw away two precious points.
There were two bookings. Rory Delap was booked for a foul in the 53rd minute and Boateng was also cautioned four minutes from time for another foul.
Phillips responded to Crouch being in the team in place of the injured James Beattie and had two other chances to add to Southampton's lead, but was foiled by Boro keeper Mark Schwarzer on both occasions.
Man of the Match: Peter Crouch - The lanky striker was given a rare chance to start for the Saints and responded with a fine dispaly and a goal to cap a fine return to the fray.